data_2TMK
#
_model_server_result.job_id            fgg4MjV6fNAi98_BJPUZgA 
_model_server_result.datetime_utc      '2024-10-26 00:25:57' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          2tmk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":217}' 
#
_entry.id    2TMK 
#
_exptl.entry_id    2TMK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.9 
_cell.angle_gamma         90 
_cell.entry_id            2TMK 
_cell.length_a            37.42 
_cell.length_b            144.2 
_cell.length_c            49.72 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2TMK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C10 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                ATM 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
P OP1 ATM doub 70 n n 
P OP2 ATM sing 71 n n 
P OP3 ATM sing 72 n n 
P O5' ATM sing 73 n n 
OP2 HOP2 ATM sing 74 n n 
OP3 HOP3 ATM sing 75 n n 
O5' C5' ATM sing 76 n n 
C5' C4' ATM sing 77 n n 
C5' H5' ATM sing 78 n n 
C5' "H5''" ATM sing 79 n n 
C4' O4' ATM sing 80 n n 
C4' C3' ATM sing 81 n n 
C4' H4' ATM sing 82 n n 
O4' C1' ATM sing 83 n n 
C3' N3' ATM sing 84 n n 
C3' C2' ATM sing 85 n n 
C3' H3' ATM sing 86 n n 
N3' N4' ATM doub 87 n n 
N4' N5' ATM doub 88 n n 
C2' C1' ATM sing 89 n n 
C2' H2' ATM sing 90 n n 
C2' "H2''" ATM sing 91 n n 
C1' N1 ATM sing 92 n n 
C1' H1' ATM sing 93 n n 
N1 C2 ATM sing 94 n n 
N1 C6 ATM sing 95 n n 
C2 O2 ATM doub 96 n n 
C2 N3 ATM sing 97 n n 
N3 C4 ATM sing 98 n n 
N3 HN3 ATM sing 99 n n 
C4 O4 ATM doub 100 n n 
C4 C5 ATM sing 101 n n 
C5 C5A ATM sing 102 n n 
C5 C6 ATM doub 103 n n 
C5A H51 ATM sing 104 n n 
C5A H52 ATM sing 105 n n 
C5A H53 ATM sing 106 n n 
C6 H6 ATM sing 107 n n 
#
_atom_sites.entry_id                     2TMK 
_atom_sites.fract_transf_matrix[1][1]    0.026724 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.010205 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006935 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.021529 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 SO4 A 1 218 218 SO4 SO4 . 
D 3 ATM A 1 217 217 ATM ATM . 
E 2 SO4 B 1 218 218 SO4 SO4 . 
F 3 ATM B 1 217 217 ATM ATM . 
G 4 HOH A 1 1030 1030 HOH HOH . 
G 4 HOH A 2 1033 1033 HOH HOH . 
G 4 HOH A 3 1036 1036 HOH HOH . 
G 4 HOH A 4 1037 1037 HOH HOH . 
G 4 HOH A 5 1038 1038 HOH HOH . 
G 4 HOH A 6 1040 1040 HOH HOH . 
G 4 HOH A 7 1048 1048 HOH HOH . 
G 4 HOH A 8 1049 1049 HOH HOH . 
G 4 HOH A 9 1053 1053 HOH HOH . 
G 4 HOH A 10 1054 1054 HOH HOH . 
G 4 HOH A 11 1059 1059 HOH HOH . 
G 4 HOH A 12 1060 1060 HOH HOH . 
G 4 HOH A 13 1061 1061 HOH HOH . 
G 4 HOH A 14 1062 1062 HOH HOH . 
G 4 HOH A 15 1063 1063 HOH HOH . 
G 4 HOH A 16 1064 1064 HOH HOH . 
G 4 HOH A 17 1065 1065 HOH HOH . 
G 4 HOH A 18 1066 1066 HOH HOH . 
G 4 HOH A 19 1068 1068 HOH HOH . 
G 4 HOH A 20 1069 1069 HOH HOH . 
G 4 HOH A 21 1070 1070 HOH HOH . 
G 4 HOH A 22 1074 1074 HOH HOH . 
G 4 HOH A 23 1075 1075 HOH HOH . 
G 4 HOH A 24 1076 1076 HOH HOH . 
G 4 HOH A 25 1077 1077 HOH HOH . 
G 4 HOH A 26 1079 1079 HOH HOH . 
G 4 HOH A 27 1080 1080 HOH HOH . 
G 4 HOH A 28 1082 1082 HOH HOH . 
G 4 HOH A 29 1088 1088 HOH HOH . 
G 4 HOH A 30 1089 1089 HOH HOH . 
G 4 HOH A 31 1090 1090 HOH HOH . 
G 4 HOH A 32 1094 1094 HOH HOH . 
G 4 HOH A 33 1095 1095 HOH HOH . 
G 4 HOH A 34 1099 1099 HOH HOH . 
G 4 HOH A 35 1100 1100 HOH HOH . 
G 4 HOH A 36 1118 1118 HOH HOH . 
G 4 HOH A 37 1119 1119 HOH HOH . 
G 4 HOH A 38 1120 1120 HOH HOH . 
G 4 HOH A 39 1121 1121 HOH HOH . 
G 4 HOH A 40 1122 1122 HOH HOH . 
G 4 HOH A 41 1123 1123 HOH HOH . 
G 4 HOH A 42 1124 1124 HOH HOH . 
G 4 HOH A 43 1125 1125 HOH HOH . 
G 4 HOH A 44 1126 1126 HOH HOH . 
G 4 HOH A 45 1127 1127 HOH HOH . 
G 4 HOH A 46 1128 1128 HOH HOH . 
G 4 HOH A 47 1129 1129 HOH HOH . 
G 4 HOH A 48 1130 1130 HOH HOH . 
G 4 HOH A 49 1131 1131 HOH HOH . 
G 4 HOH A 50 1132 1132 HOH HOH . 
G 4 HOH A 51 1133 1133 HOH HOH . 
G 4 HOH A 52 1134 1134 HOH HOH . 
G 4 HOH A 53 1136 1136 HOH HOH . 
G 4 HOH A 54 1138 1138 HOH HOH . 
G 4 HOH A 55 1140 1140 HOH HOH . 
G 4 HOH A 56 1141 1141 HOH HOH . 
G 4 HOH A 57 1143 1143 HOH HOH . 
G 4 HOH A 58 1144 1144 HOH HOH . 
G 4 HOH A 59 1145 1145 HOH HOH . 
G 4 HOH A 60 1147 1147 HOH HOH . 
G 4 HOH A 61 1149 1149 HOH HOH . 
G 4 HOH A 62 1150 1150 HOH HOH . 
G 4 HOH A 63 1151 1151 HOH HOH . 
G 4 HOH A 64 1152 1152 HOH HOH . 
G 4 HOH A 65 1164 1164 HOH HOH . 
G 4 HOH A 66 1166 1166 HOH HOH . 
G 4 HOH A 67 1175 1175 HOH HOH . 
G 4 HOH A 68 1183 1183 HOH HOH . 
G 4 HOH A 69 1186 1186 HOH HOH . 
G 4 HOH A 70 1192 1192 HOH HOH . 
G 4 HOH A 71 1208 1208 HOH HOH . 
G 4 HOH A 72 1210 1210 HOH HOH . 
G 4 HOH A 73 1211 1211 HOH HOH . 
G 4 HOH A 74 1212 1212 HOH HOH . 
G 4 HOH A 75 1214 1214 HOH HOH . 
G 4 HOH A 76 1216 1216 HOH HOH . 
H 4 HOH B 1 1001 1001 HOH HOH . 
H 4 HOH B 2 1002 1002 HOH HOH . 
H 4 HOH B 3 1003 1003 HOH HOH . 
H 4 HOH B 4 1004 1004 HOH HOH . 
H 4 HOH B 5 1005 1005 HOH HOH . 
H 4 HOH B 6 1006 1006 HOH HOH . 
H 4 HOH B 7 1007 1007 HOH HOH . 
H 4 HOH B 8 1008 1008 HOH HOH . 
H 4 HOH B 9 1009 1009 HOH HOH . 
H 4 HOH B 10 1011 1011 HOH HOH . 
H 4 HOH B 11 1012 1012 HOH HOH . 
H 4 HOH B 12 1014 1014 HOH HOH . 
H 4 HOH B 13 1015 1015 HOH HOH . 
H 4 HOH B 14 1016 1016 HOH HOH . 
H 4 HOH B 15 1017 1017 HOH HOH . 
H 4 HOH B 16 1018 1018 HOH HOH . 
H 4 HOH B 17 1019 1019 HOH HOH . 
H 4 HOH B 18 1020 1020 HOH HOH . 
H 4 HOH B 19 1021 1021 HOH HOH . 
H 4 HOH B 20 1022 1022 HOH HOH . 
H 4 HOH B 21 1023 1023 HOH HOH . 
H 4 HOH B 22 1024 1024 HOH HOH . 
H 4 HOH B 23 1025 1025 HOH HOH . 
H 4 HOH B 24 1026 1026 HOH HOH . 
H 4 HOH B 25 1027 1027 HOH HOH . 
H 4 HOH B 26 1028 1028 HOH HOH . 
H 4 HOH B 27 1032 1032 HOH HOH . 
H 4 HOH B 28 1034 1034 HOH HOH . 
H 4 HOH B 29 1035 1035 HOH HOH . 
H 4 HOH B 30 1039 1039 HOH HOH . 
H 4 HOH B 31 1041 1041 HOH HOH . 
H 4 HOH B 32 1043 1043 HOH HOH . 
H 4 HOH B 33 1044 1044 HOH HOH . 
H 4 HOH B 34 1045 1045 HOH HOH . 
H 4 HOH B 35 1046 1046 HOH HOH . 
H 4 HOH B 36 1047 1047 HOH HOH . 
H 4 HOH B 37 1050 1050 HOH HOH . 
H 4 HOH B 38 1051 1051 HOH HOH . 
H 4 HOH B 39 1052 1052 HOH HOH . 
H 4 HOH B 40 1056 1056 HOH HOH . 
H 4 HOH B 41 1057 1057 HOH HOH . 
H 4 HOH B 42 1078 1078 HOH HOH . 
H 4 HOH B 43 1092 1092 HOH HOH . 
H 4 HOH B 44 1097 1097 HOH HOH . 
H 4 HOH B 45 1102 1102 HOH HOH . 
H 4 HOH B 46 1103 1103 HOH HOH . 
H 4 HOH B 47 1104 1104 HOH HOH . 
H 4 HOH B 48 1105 1105 HOH HOH . 
H 4 HOH B 49 1106 1106 HOH HOH . 
H 4 HOH B 50 1107 1107 HOH HOH . 
H 4 HOH B 51 1108 1108 HOH HOH . 
H 4 HOH B 52 1109 1109 HOH HOH . 
H 4 HOH B 53 1110 1110 HOH HOH . 
H 4 HOH B 54 1112 1112 HOH HOH . 
H 4 HOH B 55 1113 1113 HOH HOH . 
H 4 HOH B 56 1114 1114 HOH HOH . 
H 4 HOH B 57 1115 1115 HOH HOH . 
H 4 HOH B 58 1117 1117 HOH HOH . 
H 4 HOH B 59 1153 1153 HOH HOH . 
H 4 HOH B 60 1156 1156 HOH HOH . 
H 4 HOH B 61 1157 1157 HOH HOH . 
H 4 HOH B 62 1167 1167 HOH HOH . 
H 4 HOH B 63 1168 1168 HOH HOH . 
H 4 HOH B 64 1169 1169 HOH HOH . 
H 4 HOH B 65 1170 1170 HOH HOH . 
H 4 HOH B 66 1171 1171 HOH HOH . 
H 4 HOH B 67 1174 1174 HOH HOH . 
H 4 HOH B 68 1177 1177 HOH HOH . 
H 4 HOH B 69 1178 1178 HOH HOH . 
H 4 HOH B 70 1182 1182 HOH HOH . 
H 4 HOH B 71 1185 1185 HOH HOH . 
H 4 HOH B 72 1187 1187 HOH HOH . 
H 4 HOH B 73 1188 1188 HOH HOH . 
H 4 HOH B 74 1191 1191 HOH HOH . 
H 4 HOH B 75 1193 1193 HOH HOH . 
H 4 HOH B 76 1194 1194 HOH HOH . 
H 4 HOH B 77 1195 1195 HOH HOH . 
H 4 HOH B 78 1197 1197 HOH HOH . 
H 4 HOH B 79 1200 1200 HOH HOH . 
H 4 HOH B 80 1201 1201 HOH HOH . 
H 4 HOH B 81 1202 1202 HOH HOH . 
H 4 HOH B 82 1203 1203 HOH HOH . 
H 4 HOH B 83 1204 1204 HOH HOH . 
H 4 HOH B 84 1205 1205 HOH HOH . 
H 4 HOH B 85 1206 1206 HOH HOH . 
H 4 HOH B 86 1207 1207 HOH HOH . 
H 4 HOH B 87 1209 1209 HOH HOH . 
H 4 HOH B 88 1213 1213 HOH HOH . 
H 4 HOH B 89 1215 1215 HOH HOH . 
H 4 HOH B 90 1217 1217 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P P ATM . . . D 3 4.099 36.776 4.978 1 17.85 ? P ATM 217 A 1 
HETATM 2 O OP1 ATM . . . D 3 5.078 35.828 5.518 1 14.97 ? OP1 ATM 217 A 1 
HETATM 3 O OP2 ATM . . . D 3 3.195 37.531 5.905 1 25.7 ? OP2 ATM 217 A 1 
HETATM 4 O OP3 ATM . . . D 3 5.004 37.776 4.138 1 26.81 ? OP3 ATM 217 A 1 
HETATM 5 O O5' ATM . . . D 3 3.043 36.089 4.013 1 18.32 ? O5' ATM 217 A 1 
HETATM 6 C C5' ATM . . . D 3 3.412 35.11 3.039 1 17.41 ? C5' ATM 217 A 1 
HETATM 7 C C4' ATM . . . D 3 2.218 34.716 2.165 1 14.79 ? C4' ATM 217 A 1 
HETATM 8 O O4' ATM . . . D 3 1.493 33.575 2.631 1 15.81 ? O4' ATM 217 A 1 
HETATM 9 C C3' ATM . . . D 3 1.207 35.845 1.962 1 11.66 ? C3' ATM 217 A 1 
HETATM 10 N N3' ATM . . . D 3 1.063 36.058 0.544 1 24.16 ? N3' ATM 217 A 1 
HETATM 11 N N4' ATM . . . D 3 1.577 36.875 -0.249 1 35.18 ? N4' ATM 217 A 1 
HETATM 12 N N5' ATM . . . D 3 2.026 37.588 -0.94 1 41.81 ? N5' ATM 217 A 1 
HETATM 13 C C2' ATM . . . D 3 -0.087 35.217 2.35 1 8.54 ? C2' ATM 217 A 1 
HETATM 14 C C1' ATM . . . D 3 0.158 33.752 2.114 1 15.02 ? C1' ATM 217 A 1 
HETATM 15 N N1 ATM . . . D 3 -0.739 33.018 2.989 1 18.67 ? N1 ATM 217 A 1 
HETATM 16 C C2 ATM . . . D 3 -1.626 32.117 2.419 1 24.07 ? C2 ATM 217 A 1 
HETATM 17 O O2 ATM . . . D 3 -1.737 31.917 1.213 1 21.5 ? O2 ATM 217 A 1 
HETATM 18 N N3 ATM . . . D 3 -2.369 31.382 3.323 1 26.22 ? N3 ATM 217 A 1 
HETATM 19 C C4 ATM . . . D 3 -2.137 31.298 4.694 1 26.6 ? C4 ATM 217 A 1 
HETATM 20 O O4 ATM . . . D 3 -2.72 30.463 5.368 1 21.21 ? O4 ATM 217 A 1 
HETATM 21 C C5 ATM . . . D 3 -1.156 32.234 5.203 1 24.02 ? C5 ATM 217 A 1 
HETATM 22 C C5A ATM . . . D 3 -0.924 32.327 6.698 1 14.21 ? C5A ATM 217 A 1 
HETATM 23 C C6 ATM . . . D 3 -0.534 33.068 4.355 1 19 ? C6 ATM 217 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           23 
#